The city Department of Investigation has been quietly attending City Council hearings without informing members, The Post has learned.

Council members, already on edge over the ongoing probe into a secret slush fund, were startled by the presence of a prober at a routine Finance Committee hearing this week.

Speaker Christine Quinn, committee Chairman David Weprin (D-Queens) and other members at the hearing told The Post afterward they were unaware an investigator was in attendance.

“I’ve been involved in [city] government since 1997, and I’ve never heard of this being the case,” one council member who attended the hearing said.

“I just think it’s a not-so-subtle intimidation factor to send the message to all members that Big Brother is watching.”

A City Hall source who confirmed the investigator’s presence said DOI employees typically sit in on council hearings without announcing their presence. A DOI spokeswoman declined comment.

Most members assumed the investigator was gathering information for a probe into the council’s practice of squirreling taxpayer money into fake groups, only to dish out the funds to favored members later in the year.

The budgeting trick is at the center of a dual investigation by the DOI and the US Attorney’s Office, which already has indicted two staffers to Councilman Kendall Stewart (D-Brooklyn) for allegedly stealing public money, some of which was parked in fictitious organizations.

The investigation is a blow to Quinn’s political career as she contemplates a bid for mayor next year.

“Maybe DOI routinely does send people to council hearings. I’ve never heard of that,” Councilman David Yassky (D-Brooklyn) said.

“I’ve not talked to anybody at DOI, but I’m sure that they’re trying to gather all the information they can about the process of allocating discretionary funds in the City Council.”

Peter Vallone Jr., a Democratic councilman from Queens, joked, “I couldn’t think of a more boring topic than a budget mod [modification], so I assume they weren’t there for the entertainment value.”

He defended the agency’s right to attend the hearing without announcing itself.

“I have no problem with their not informing them that they were there, and I wish them well in their investigation,” Vallone said.

Dick Dadey, head of government watchdog group Citizens Union and a close ally of Quinn, criticized the secrecy.

“If it is routine, then it would seem as if the practice would have been known to the City Council,” Dadey said.

“I mean, the committees are open to the public, but a member of the DOI staff sits in not just as a member of the public, but with a purpose in mind that may be hidden.”